Running Aquamacs 3.0a on Mac OS X 10.8.5, I used customize-faces to change the background and foreground and to pick a nice font. Aquamacs added the following lines to a file it created called ~/Library/Preferences/Aquamacs Emacs/customizations.el:

(custom-set-faces
;; custom-set-faces was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(default ((t (:background "Black" :foreground "White" :height 130 :family "Menlo"))))
'(mode-line ((t (:background "grey75" :foreground "black" :box nil)))))

I also used customize to deactivate autofaces and Aquamacs duly added '(aquamacs-autoface-mode nil) to the custom-set-variables form in the same file.

Upon restarting Aquamacs these customizations aren't in effect. Instead it decides to give me black background and foreground --black is a fine color, but using it for both foreground and background is clearly too much of a good thing.

Running M-x load-file "~/Library/Preferences/Aquamacs Emacs/customizations.el", as I expected, applies my settings. I currently put the following function definition in my ~/Library/Preferences/Aquamacs Emacs/Preferences.el:

and manually run M-x fix-aquamacs every time I have to restart it (which is not often). Does anyone know what is happening? My guesses:

Aquamacs puts stuff in customizations.el but doesn't load it! (This is clearly wrong, I can't believe Aquamacs would do that.)

Something else is changing the fonts after Aquamacs loads customizations.el, but what? My Preferences.el does not contain anything related to faces, I don't have a ~/.emacs or ~/.emacs.d/init.el. Is there some other file Aquamacs loads at startup? Does it also get ideas about fonts and colors from some Mac OS X system settings? (I am clueless about Mac OS X, I only use Macs ocasionally.)